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The Canonical Motif Is a Rossmann-Fold Identifier

Nearly half of the structures (279/578) in our original dataset were found to have the canonical carboxylate-ribose interaction but had no SCOP or CATH category ( Isabel Marant Zebre Shoes Suede Pumps Free Shipping Marketable Cheap Looking For 100% Authentic Cheap Price With Mastercard 2018 For Sale AYp3mQ47b
). We manually examined all 279 structures and found that 271 of these structures have a Rossmann, or Rossmann-like, topology, as defined above, and with the interacting Glu/Asp located at the tip of β2 ( S5 and From China Free Shipping Extremely MCM Leather Moto Boots Discount Recommend gr85h0
Tables, S7 Fig ). In fact, 108 out of the 279 structures that were not annotated in the CATH version v3.5.0 used to make our dataset are annotated in the current version (v.4.0.0; in which the number of annotated domains is larger by 36%). This “blind test” indicates that the applied criteria are sufficient not only to identify the canonical motif in Rossmann enzymes but also to rigorously identify a Rossmann enzyme merely by the existence of this canonical motif.

NAD-utilizing enzymes provide another indication for divergence from a common adenosine-binding ancestor. The cofactor NAD contains two riboses, one attached to adenosine and the other to nicotinamide. However, in the 259 available structures of NAD-dependent enzymes, only bidentate carboxylate-ribose interaction was found with the ribose. Among the NAD enzymes annotated as Rossmann, 145 structures out of 155 fit the canonical criteria with respect to the interaction with the adenosine’s ribose ( S7 Table ). Only four structures possess an additional bidentate interaction with NAD’s nicotinamide ribose. Of these four, two are annotated as Rossmann folds. Both these structures have one canonical interaction at the tip of β2 binding the adenosine ribose, as do the 145 other NAD Rossmann-fold enzymes. The nicotinamide riboses, however, interact with Glu residues located not at the tip of β2, and these bidentate interactions exhibit noncanonical geometries ( Fig 3A and Charlotte Olympia CapToe Suede Pumps Cheap Footlocker Cheap Sale Footaction Lowest Price Cheap Price VnFeROfUud
). The variability of the ribose-carboxylate angles and topology (Asp/Glu locations other than β2) and the sporadic presence (4/155 indicating appearance in recently evolved lineages) are all consistent with emergence by convergence. In contrast, the prevalence (145/155) and conservation of both geometry and topology of the interaction with the adenosine’s ribose most likely indicates divergence from a primordial ancestor of the Rossmann fold.

Fig 3. Representative noncanonical bidentate interactions in Rossmann and non-Rossmann enzymes.

(A) Zoom-in view of the structure of L-3-hydroxyacyl-CoA dehydrogenase belonging to the Rossmann fold (PDB 1F17). The cofactor, NAD (in green sticks), has its adenosine ribose interacting with D53 located at the tip of β2, with a canonical angle (α = 120°). A second bidentate interaction is observed that is not observed in other Rossmann NAD dehydrogenases, between the nicotinamide ribose and E114 located on H4 and with a noncanonical angle (α = 16°). (B) Zoom-in view of the HIT protein (HINT, histidine triad), a non-Rossmann enzyme in which a carboxylate-ribose bidentate is observed (PDB 3RHN). The cofactor, adenosine monophosphate (AMP), is in cyan sticks. The interacting D43 is at the tip of a β-strand and with a canonical angle (α = 116°). Note, that the β-strand is part of an antiparallel sheet, in oppose to the parallel β-sheet that comprises the Rossmann’s core ( Fig 1 ).

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